seqforge 2026.7.1__py3-none-any.whl

seqforge-2026.7.1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: seqforge
+Version: 2026.7.1
+Summary: Compile arbitrary FASTQ + messy metadata into a validated, machine-independent sequencing library manifest and a runnable Snakemake config.
+Project-URL: Homepage, https://github.com/liuhlab/seqforge
+Project-URL: Issues, https://github.com/liuhlab/seqforge/issues
+Project-URL: Changelog, https://github.com/liuhlab/seqforge/blob/main/CHANGELOG.md
+Author: Liu Lab
+License-Expression: MIT
+License-File: LICENSE
+Keywords: bioinformatics,fastq,manifest,single-cell,snakemake
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.12
+Requires-Dist: anndata>=0.10
+Requires-Dist: anthropic>=0.40
+Requires-Dist: numpy>=2
+Requires-Dist: openai>=1.40
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: pdfplumber>=0.11
+Requires-Dist: pooch>=1.8
+Requires-Dist: pydantic>=2.7
+Requires-Dist: pymupdf>=1.24
+Requires-Dist: pypdf>=4
+Requires-Dist: pyyaml>=6
+Requires-Dist: requests>=2.31
+Requires-Dist: tqdm>=4
+Requires-Dist: typer>=0.12
+Description-Content-Type: text/markdown
+
+<!-- A centered, sized logo and title need inline HTML and precede the first heading, which the
+     default ruleset forbids (MD033, MD041). Scope the exception to this masthead; every other rule
+     stays on for the README. -->
+<!-- markdownlint-disable MD033 MD041 -->
+<p align="center">
+  <img src="docs/assets/logo-readme.png" alt="seqforge" width="200">
+</p>
+
+<h1 align="center">seqforge</h1>
+<!-- markdownlint-enable MD033 MD041 -->
+
+Compile `(arbitrary FASTQ files) + (unstructured human/DB metadata)` into a validated,
+machine-independent **dataset manifest**, then into a runnable Snakemake config — for headless
+reprocessing of large collections of public sequencing datasets into a genomic-AI training corpus.
+
+**seqforge is a compiler, not a chatbot.** Deterministic code owns every decision. The LLM has
+exactly two jobs: parse prose into span-verified assertions, and arbitrate ambiguity the
+deterministic layer has *already flagged*. Everything else is a verifier.
+
+```text
+probe(files)                           -> Observation   deterministic, no LLM, no network, bytes only
+harvest(prose, instructions)           -> Assertion     LLM, each claim span-verified
+resolve(Observations, KB, hypothesis?) -> candidates, Conflicts, Questions, Blockers
+──────────────────────────────────────────────────────────────────────────────────────────────────
+  => manifest.yaml     what the data IS.   One per dataset. Immutable, content-addressed.
+
+plan(Assertions, flags, policy)        -> ProcessingSection   flag > instruction > policy
+──────────────────────────────────────────────────────────────────────────────────────────────────
+  => processing.yaml   what to DO with it. Many per dataset.
+
+compose(manifest, processing)          -> config.yaml + units.tsv + module selection
+```
+
+Same dataset + a different recipe = a different pipeline, and the dataset's hash **does not move**.
+
+The files can be local or remote: `seqforge io probe-remote <url>` fingerprints a library straight
+from a URL via one bounded HTTP Range read — same identification, no download.
+
+**Status: the pilot compiles end to end.** The deterministic spine is implemented and green
+(`pixi run check`), and `seqforge run` takes the worm pilot PRJNA1027859 from its raw FASTQs and paper
+to a validated manifest + a runnable Snakefile in one headless pass. The ground-truth alignment runs
+(`kb e2e`) are still on synthetic yeast/worm fixtures with injected counts — it has not yet executed a
+pipeline on real reads at scale.
+
+Docs: **<https://liuhlab.github.io/seqforge/>** · design + rationale + scope delta:
+[`docs/design.md`](docs/design.md) (its §9 is the running list of what is *not* yet built) · rules:
+[`CLAUDE.md`](CLAUDE.md)
+
+## Install
+
+```bash
+pip install seqforge
+```
+
+This gives you the compiler and the `seqforge` CLI. The two lab-only stages — `compose` against a real
+genome and `kb e2e` — additionally need the lab's `liulab-genome` and `liulab-data` packages, which are
+not on PyPI. Install them from git when you need those features:
+
+```bash
+pip install "liulab-genome @ git+https://github.com/liuhlab/liulab-genome.git" \
+            "liulab-data   @ git+https://github.com/liuhlab/liulab-data.git"
+```
+
+(Inside the lab, `pixi install` already pulls both — see below.)
+
+## Develop
+
+Everything runs through [pixi](https://pixi.sh) (not `pip`/`conda`/`venv`):
+
+```bash
+pixi install                     # build environments
+pixi run test                    # pytest
+pixi run lint                    # ruff check .
+pixi run typecheck               # mypy --strict on models/, probe/, resolve/, manifest/,
+                                 #   compose/, workflows/, harvest/, evals/
+pixi run check                   # lint + fmt-check + typecheck + test
+pixi run -- pre-commit install   # once per clone — ruff, mypy, shellcheck (not the suite)
+```
+
+Most of the non-negotiable rules in `CLAUDE.md` are enforced by tests, so `pixi run check` is the
+mechanism rather than a formality — and CI runs it on every push and PR. The pre-commit hooks are
+deliberately limited to the fast ones, so run `check` yourself when you change behaviour.
+
+## Consumer of the liulab stack
+
+seqforge references genomes by a `liulab-genome` UCSC assembly id + registered GTF name, and aligner
+environments by their literal `liulab-runtime` name (`align-rna`, ...). It never defines genome-file
+machinery or aligner environments itself — and there is a test that says so.

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+seqforge/workflows/qc.py,sha256=uPro9Ma0L35etXF0s7Rx5Yw2a4TjwqhzoAt0J4nuovA,6095
+seqforge/workflows/map/star.smk,sha256=uoSzrdc5L_g6hZnQkc8tTazfCI6WOux2xeaDFLMpsm4,4677
+seqforge/workflows/map/starsolo.smk,sha256=ITXi2bYb-kOjIrY1LAV1aZYNGHiHFYoIMUFUoTBEPj8,18902
+seqforge-2026.7.1.dist-info/METADATA,sha256=-SY8UtxMG6ON2Ekdbu3CDEPIuwYj_3EE_haSWr9fYoQ,6281
+seqforge-2026.7.1.dist-info/WHEEL,sha256=lCkmxWfQsSc9CfIClYeavTdQeEX2toPqufh9gI35EQA,87
+seqforge-2026.7.1.dist-info/entry_points.txt,sha256=pQptwtL5F2LFrRG3h4BbWud3JHgjSjw3nevi91v6on8,46
+seqforge-2026.7.1.dist-info/licenses/LICENSE,sha256=YqrYteEs2ICOm_LU9wLTCWngjkabTAbpEDae3cmVDac,1064
+seqforge-2026.7.1.dist-info/RECORD,,

seqforge-2026.7.1.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.31.0
+Root-Is-Purelib: true
+Tag: py3-none-any

seqforge-2026.7.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+seqforge = seqforge.cli:app

seqforge-2026.7.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Liu Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.